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What makes a good DNA barcode?

In the original paper presenting the concept of DNA barcoding, Paul Hebert and colleagues discussed the reasons why mitochondrial genes were preferable to nuclear genes for the purposes of DNA barcoding in animals: unlike nuclear genes, mitochondrial genes lack introns, are generally haploid, and exhibit limited recombination (Hebert et al. 2003). Although insertions and deletions are prevalent in mitochondrial genes encoding ribosomal DNA, they are extremely uncommon in mitochondrial genes encoding proteins, greatly facilitating alignment of the latter (Hebert et al. 2003). 

Of the thirteen protein-coding genes present on the animal mitochondrial genome, Hebert et al. (2003) proposed the use of cytochrome oxidase I (referred to simply as “COI”) as a barcode marker for animals for two reasons. First, robust primers make COI easy to amplify for a broad spectrum of phyla. Secondly, the rate of nucleotide substitution is high enough to distinguish not only among closely related species but also among different populations of the same species. At the present time, COI is recognized by iBOL (the International Barcode of Life Project) as the official barcode marker for animals.

 In other groups of organisms, however, COI does not perform well as a DNA barcode. In plants and fungus, for example, COI is either too invariable (a problem in both groups) or may contain large introns (a problem in fungus) (Kress et al. 2005; Chase et al. 2007; Schoch et al. 2012). The nuclear gene ITS1/2 is presently recognized by iBOL as the official barcode marker for fungus; two genes located on the chloroplast genome, rbcL and matK, are the official barcodes in plants.
 
An ideal barcode marker should also be easy to amplify and align. To facilitate amplification, a DNA barcode should have conserved primer sites in the DNA regions flanking the target gene such that the same primer pairs may be used across a wide spectrum of organisms (so-called “universal” primers). It is often desirable to use markers that are present in multiple copies; this may make them easier to amplify from DNA extractions based on older material (e.g. the type of material often found in museum collections). Finally, ideal barcode markers should be easy to align; this faciliates tree-based species identification, one of the most commonly used methods of identifying species using DNA barcodes. 
 
References

Chase, M.W., R.S. Cowan, P.M. Hollingsworth, C. van den Berg, S. Madriñán, et al. 2007. A proposal for a standardised protocol to barcode all land plants. Taxon 56(2): 295-299.
 
Hebert, P.D.N., A. Cywinska, S.L. Ball, and J.R. deWaard. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London B - Biological Sciences 270: 313-321.
 
Kress, W.J., K.J. Wurdack, E.A. Zimmer, L.A. Weigt, and D.H. Janzen. 2005. Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences USA 102 (23) : 8369–8374.
 
Schoch, C.L., K.A. Seifert, S. Huhndorf, V. Robert, J.L. Spouge, C.A. Levesque, W. Chen; Fungal Barcoding Consortium; Fungal Barcoding Consortium Author List. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences USA 109(16): 6241-6246.